Fantasy or sci-fi route?

This is a very rough draft of the story idea I've been working on for a few years. I haven't actually written any of the story down yet properly, so large parts of the details are undecided. Apologies if it's too long to read, it's rather complicated. Basically, I'd like to know your opinions on the genre. I've been trying to decide between fantasy and scifi elements. Feel free to give any feedback that comes to your mind!

At the time when the story begins, humans have been living on an alternate version of Earth, let's call it Earth Two for now, for a few hundred years. The original, Earth One, was destroyed by causes such as pollution and overpopulation etc, and a group of different nations collaborated together to create a way for some of the humans to travel to an alternate Earth to save humanity. Earth Two is fairly similar to Earth One, except for some minor geological differences and new kinds of flora and fauna. Oh, and of course, a new race that inhabits Earth Two instead of humans.

This is where I need to decide whether to go with the more fantasy-route or the more scifi route. The race could either be something like the Neanderthals, with only slight differences to modern humans in terms of abilities, behaviour and looks, or something entirely different, such as a humanoid race that has (for example) plant-like qualities, abilities, or even magic. Either way, the race outnumbers the new humans in the start, and humans have to work together with the natives to learn to live on Earth Two. They receive geographical information, and info about local flora and fauna (and potentially about magic), and in return they teach advanced science to the natives.

The humans that arrived on Earth Two were carefully selected and hand picked by the nations that worked together on the project. Only those who were from the right countries, or had power/money to pay for the journey could travel to the parallel reality and be saved from their ultimate demises on Earth One. And the newly formed government was very strict, making sure that no unwanted ideas from Earth One made their way to their new paradise. They basically re-wrote history, and even some science. (Hitler? Who's that?) However, despite their best efforts, not everyone in the new society could be rich and powerful. Population began rising alarmingly quickly again, especially among the poor who lived on the outer edges of the cities. And those native habitants of Earth Two? They were basically second class citizens.

The main character of the story is a descendant of the native race of Earth Two. This will prove to be important later for genetic reasons, because at the start of the story, humans have braved to the arctic regions of Earth Two and uncovered an old giant virus from deep ice. This is incidentally what killed homo sapiens of Earth Two originally. The virus starts an infection that creates a zombie-like-state for the infected, making them attack people in large masses. This makes the infection spread quickly and kills lot of non-infected people in the riot-like attacks, especially in the heavily populated outer edges of the cities.

The main character's town is overrun by "zombies", however MC survives. MC is bit and banged up in the atttack, and a kind Doctor patches them up. The Doctor eventually realises something in MC's blood makes the MC immune, so he figures out there must be a cure. However, certain key members of the government see this as a way to get rid of the ever-rising population, and as they hear about the Doctor's idea of a cure, they assassinate him. However, the Doctor has already told MC about the cure, and they embark on a journey to create a cure and create a revolution. Unknown to MC, there is a secret society of people who have been preserving knowledge from Earth One, and these & some other people he meets on his journey will help him overthrow the rotten government and save humanity from nearby extinction (again).

The story is a strange mix of dystopian sci-fi and fantasy, in an alternate reality, involving zombie-like infected people for added thrills. I know it probably sounds like it has a lot of clichés, but as I said, it's just a rough draft of the story I'd like to tell.

My problem is this: I originally started with a fantasy story idea, but it seems to be turning into science-fiction every time I try to develop it. Originally the main character was part of genetically mutated group of people who had developed superpowers and such (think X-men, but more Harry Potter, where people might be able shapeshift into animals) which was why they were shunned by the rest of the society. Now the MC is part of an entirely new race of humanoid beings, and I can make them down-to-earth realistic with the Neanderthal route, or go for the fantasy route and add magic or paranomal powers and other weird things.

Which one out of these two possibilities would you rather pick up? Which would work better with the plot and world I just described?

It doesn't seem like a rigid "scientific" background is important to how this story is told, though a consistent world with strict rules will matter. You can build the setting with whatever elements you want, then decide afterwards whether those elements are close enough to real-life science to classify as "science fiction." (And don't forget Clarke's Third Law--a new world with parallel evolution and tech could justify inventions and abilities that seem magical to the newcomers.)